# Package picard.arrays.illumina

package picard.arrays.illumina

Related Packages
Package
Description
picard.arrays
Class
Description
ArraysControlInfo
A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
BpmToNormalizationManifestCsv
A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .
Build37ExtendedIlluminaManifest
A class to represent an 'Extended' Illumina Manifest file.
Build37ExtendedIlluminaManifestRecord
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
Build37ExtendedIlluminaManifestRecord.Flag
Build37ExtendedIlluminaManifestRecordCreator
CompareGtcFiles
A simple tool to compare two Illumina GTC files.
CreateExtendedIlluminaManifest
Create an Extended Illumina Manifest by performing a liftover to Build 37.
IlluminaAdpcFileWriter
A class to encompass writing an Illumina adpc.bin file.
IlluminaAdpcFileWriter.Record
IlluminaBPMFile
A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
IlluminaBPMLocusEntry
A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file
IlluminaGenotype
IlluminaManifest
A class to represent an Illumina Manifest file.
IlluminaManifestRecord
A class to represent a record (line) from an Illumina Manifest [Assay] entry
IlluminaManifestRecord.IlluminaStrand
InfiniumDataFile
A class to provide methods for accessing Illumina Infinium Data Files.
InfiniumEGTFile
A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls
InfiniumFileTOC
A class to encapsulate the table of contents for an Illumina Infinium Data Files.
InfiniumGTCFile
A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
InfiniumGTCRecord
InfiniumNormalizationManifest
A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
InfiniumTransformation
InfiniumVcfFields
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
InfiniumVcfFields.GENOTYPE_VALUES